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Sample GSM184248 Query DataSets for GSM184248
Status Public on Aug 09, 2007
Title OVX-34 vs 26695/J99 mix
Sample type genomic
 
Channel 1
Source name 0.25 ug 26695 + 0.25 ug j99 genomic DNA
Organism Helicobacter pylori
Characteristics 0.25 ug 26695 + 0.25 ug j99 genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name 0.5 ug genomic DNA OVX-34
Organism Helicobacter pylori
Characteristics 0.5 ug genomic DNA OVX-34
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1840, 9130; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nina,,Salama
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.55; Parameter Scan Time = 11:45:51; Parameter PMT Volts = 630; Parameter Scan Date = 2006-06-09; Parameter Pixel Size = 10; Parameter Laser on time = 86935; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.47; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.55; Parameter Scan Time = 11:45:51; Parameter PMT Volts = 760; Parameter Scan Date = 2006-06-09; Parameter Pixel Size = 10; Parameter Laser on time = 87362; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.65; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68907.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Apr 25, 2007
Last update date Aug 08, 2007
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL5124
Series (1)
GSE7618 Array CGH of Mexican Patient Isolates and BCS100 Strain

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 3755 4963 3768 4960 -13 3 3763 5003 3894 5038 -5 43 0 0 1277 1468 1192 1415 18 13 3 5 -10 38 null null null .882 .92 2.682 80 546 1.843 .35 100 2190 9860 68 78 30 40 0 4817 4814 3 null 4856 42 null null null null
2 6075 8184 4796 6351 1279 1833 6176 7946 4739 6440 1380 1595 0 0 1164 1203 1221 1589 50 50 16 25 3112 2975 .698 1.433 1.156 1.777 1.571 5.083 12 104 2.038 .15 50 2450 9850 69 74 58 63 0 7943 6164 1779 1.391 7712 1548 .719 1.122 .476 .166
3 15499 21163 4641 5824 10858 15339 13601 18738 4837 6072 8960 12914 0 0 6216 7203 1435 1615 100 99 98 99 26197 21874 .708 1.413 1.441 1.469 1.515 1.493 208 1350 1.358 .89 160 2720 9850 64 80 80 96 0 20540 5653 14887 1.371 18186 12534 .729 1.399 .455 .484
4 5889 7308 5317 7121 572 187 5873 7108 5557 7318 556 -13 0 0 1799 1876 1573 1773 27 21 8 6 759 543 3.059 .327 null .901 .974 4.306 80 560 1.399 .25 100 2970 9850 67 77 108 118 0 7093 6911 181 .317 6899 -13 3.152 null -1.656 null
5 10444 13681 5378 7001 5066 6680 10600 13746 5642 7227 5222 6745 0 0 1926 2598 1662 1810 95 97 82 85 11746 11967 .758 1.319 1.292 1.323 1.267 1.871 208 1469 1.36 .72 170 3230 9830 61 78 130 147 0 13278 6795 6483 1.28 13341 6546 .781 1.254 .356 .326
6 9126 9652 5760 7425 3366 2227 8977 9415 6026 7626 3217 1990 0 0 2069 2113 1722 1740 76 52 43 29 5593 5207 1.511 .662 .619 .718 .803 2.408 156 1021 .779 .4 140 3500 9800 60 74 159 173 0 9368 7206 2161 .642 9138 1931 1.557 .6 -.639 -.736
7 12428 16170 6208 7869 6220 8301 12374 15984 6480 8077 6166 8115 0 0 3003 3339 1716 1852 94 97 81 92 14521 14281 .749 1.335 1.316 1.428 1.341 1.938 256 1534 1.346 .79 180 3760 9820 60 78 183 201 0 15694 7637 8057 1.295 15513 7876 .772 1.277 .373 .353
8 7768 9883 7260 8749 508 1134 7842 9686 7360 8972 582 937 0 0 1875 2303 1724 1992 27 35 2 11 1642 1519 .448 2.232 1.61 1.163 1.17 3.495 80 560 2.097 .25 100 4030 9810 63 73 214 224 0 9592 8491 1101 2.167 9401 909 .462 1.563 1.115 .644
9 8905 11956 8532 10376 373 1580 8724 11643 8828 10515 192 1267 0 0 1799 2151 1905 1966 18 37 6 15 1953 1459 .236 4.236 6.599 1.282 .996 7.093 32 176 2.178 .24 60 4300 9800 64 70 243 249 0 11604 10070 1533 4.111 11300 1230 .243 6.405 2.04 2.679
10 9725 12570 8538 10903 1187 1667 10132 12691 8692 10952 1594 1788 0 0 1852 1976 1768 1892 43 50 9 18 2854 3382 .712 1.404 1.122 .886 1.212 2.437 32 176 1.901 .31 60 4540 9820 66 72 267 273 0 12200 10582 1618 1.363 12317 1735 .734 1.089 .447 .123
11 14958 19215 7039 8505 7919 10710 12805 17272 7218 8766 5766 8767 0 0 5618 6355 1768 1910 96 99 82 92 18629 14533 .739 1.352 1.52 1.411 1.393 1.691 208 1373 1.28 .84 160 4790 9800 59 75 287 303 0 18649 8255 10395 1.313 16763 8509 .762 1.476 .392 .561
12 13369 18037 6794 8068 6575 9969 13440 17936 7016 8258 6646 9868 0 0 1844 2546 1712 1676 99 100 94 99 16544 16514 .66 1.516 1.485 1.532 1.501 1.364 156 1052 1.543 .82 150 5050 9800 59 74 313 328 0 17506 7830 9675 1.472 17408 9577 .68 1.441 .557 .527
13 12706 10965 7281 8565 5425 2400 11629 10756 7678 8846 4348 2191 0 0 3953 2034 2135 1894 82 55 51 23 7825 6539 2.26 .442 .504 .453 .52 3.986 156 1225 .364 .4 150 5310 9740 53 68 339 354 0 10642 8313 2329 .429 10439 2126 2.329 .489 -1.22 -1.032
14 11213 11323 8498 9716 2715 1607 11387 10865 8824 9889 2889 1149 0 0 2431 2240 2582 2074 51 38 15 15 4322 4038 1.689 .592 .398 .603 .729 4.396 80 532 .689 .43 100 5590 9770 59 69 370 380 0 10990 9430 1560 .574 10545 1115 1.741 .386 -.8 -1.373
15 15333 18552 7915 9339 7418 9213 14970 18427 8117 9527 7055 9088 0 0 3018 4034 1886 1980 98 98 93 91 16631 16143 .805 1.242 1.288 1.203 1.263 1.611 256 1585 1.271 .83 180 5820 9770 55 73 389 407 0 18006 9064 8942 1.205 17884 8820 .83 1.25 .27 .322
16 12382 13670 8825 10518 3557 3152 11173 11641 9172 11035 2348 1123 0 0 5756 7333 2304 2703 51 31 23 20 6709 3471 1.128 .886 .478 1.009 1.09 3.743 80 554 1.296 .75 100 6070 9790 61 71 418 428 0 13267 10208 3059 .86 11298 1090 1.163 .464 -.218 -1.107
17 10732 9900 3702 4849 7030 5051 10883 9905 3860 4968 7181 5056 0 0 1778 1832 1224 1491 100 99 98 87 12081 12237 1.392 .718 .704 .698 .705 1.552 208 1274 .727 .75 160 2200 10090 88 104 28 44 0 9609 4706 4902 .697 9613 4907 1.434 .683 -.52 -.549
18 9771 12297 4286 5809 5485 6488 9554 11959 4546 5935 5268 6150 0 0 2195 2682 1360 1486 99 99 92 91 11973 11418 .845 1.183 1.167 1.178 1.193 1.597 208 1201 1.258 .76 160 2470 10090 88 104 55 71 0 11935 5638 6297 1.148 11607 5969 .871 1.133 .199 .18
19 9012 12546 4915 6549 4097 5997 9105 12657 5078 6807 4190 6108 0 0 1801 2650 1457 1673 90 96 75 79 10094 10298 .683 1.464 1.458 1.395 1.467 1.951 120 728 1.639 .65 120 2720 10090 90 102 82 94 0 12177 6356 5820 1.421 12284 5928 .704 1.415 .507 .501
20 9356 13498 5842 7720 3514 5778 9277 13396 6058 7890 3435 5676 0 0 1911 2806 1645 1931 82 90 52 75 9292 9111 .608 1.644 1.652 1.736 1.61 2.071 120 804 1.799 .61 120 3000 10120 93 105 110 122 0 13101 7493 5608 1.596 13002 5509 .627 1.604 .674 .681

Total number of rows: 4032

Table truncated, full table size 1012 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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